Journal Articles

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2017

  • Klamt, S., Mahadevan, R. and Hädicke, O. (2017), When Do Two-Stage Processes Outperform One-Stage Processes?, Biotechnology Journal, 1700539. doi:10.1002/biot.201700539. Click here.
  • Garg, S., Judd, K., Mahadevan, R., Edwards, E., & Papangelakis, V. G. (2017). Leaching characteristics of nickeliferous pyrrhotite tailings from the Sudbury, Ontario area. Canadian Metallurgical Quarterly, 56(4), 372-381. doi:10.1080/00084433.2017.1361162. Click here.
  • S. Partow, P. Hyland, R. Mahadevan. 2017. Synthetic rescue couples NADPH generation to metabolite overproduction in Saccharomyces cerevisiae. Metabolic Engineering, Accepted Manuscript. Click here.
  • Khusnutdinova, A. N., Flick, R., Popovic, A., Brown, G., Tchigvintsev, A., Nocek, B., Correia, K., Joo, J. C., Mahadevan, R. and Yakunin, A. F. (), Exploring bacterial carboxylate reductases for the reduction of bifunctional carboxylic acids. Biotechnology Journal, 1700015. Accepted Author Manuscript. doi:10.1002/biot.201600751. Click here.
  • S. Klamt, G. Regensburger, M.P. Gerstl, C. Jungreuthmayer, S. Schuster, R. Mahadevan, J.Zanghellini, S. Müller, From elementary flux modes to elementary flux vectors: metabolic network and pathway analysis with arbitrary linear flux constraints. PLoS Computational Biology, 13 (2017). Click here.
  • Kim T, Flick R, Brunzelle J, Singer A, Evdokimova E, Brown G, Joo JC, Minasov GA, Anderson WF, Mahadevan R, Savchenko A, Yakunin AF. 2017. Novel aldo-keto reductases for the biocatalytic conversion of 3-hydroxybutanal to 1,3-butanediol: structural and biochemical studies. Applied Environmental Microbiology 83:e03172-16. Click here.
  • Wang, P., Tang, S., Nemr, K., Flick, R., Yan, J., Mahadevan, R., Yakunin, A.F., Loffler, F.E., Edwards, E. A. (2016). Refined experimental annotation reveals conserved corrinoid autotrophy in chloroform-respiring Dehalobacter isolates. The ISME Journal,11(3), 626-640. doi:10.1038/ismej.2016.158. Click here.
  • Garg, S., Papangelakis, V., Edwards, E., Mahadevan, R., (2017). Application of a selective dissolution protocol to quantify the terminal dissolution extents of pyrrhotite and pentlandite from pyrrhotite tailings. International Journal of Mineral Processing, 158, 27-34. Click here.
  • Pandit AV, Srinivasan S, Mahadevan R. Redesigning metabolism based on orthogonality principles. Nature Communications 2017;8:15188. doi:10.1038/ncomms15188. Click here.
  • J.C. Joo, et al. Alkene hydrogenation activity of enoate reductases for an environmentally benign biosynthesis of adipic acid. Chemical Sciences, 8 (2016), pp. 1406-1413. Click here.

2016

  • Toroghi M. K., Cluett W. R. , Mahadevan R. Multiscale Metabolic Modeling Approach for Predicting Blood Alcohol Concentration. IEEE Life Sciences Letters 2016 2(4): 59-62. Click here.
  • Wang P. H., Tang S., Nemr K., Flick R., Yan J., Mahadevan R., et al. (2017). Refined experimental annotation reveals conserved corrinoid autotrophy in chloroform-respiring Dehalobacter isolates. ISME Journal 11 626–640. 10.1038/ismej.2016.158. Click here.
  • Rodenhizer D, Gaude E, Cojocari D, et al. A 3D engineered tumour for spatial snap-shot analysis of cell metabolism and phenotype in hypoxic gradients. Nature Materials 2016 ;15(2):227-234. doi:10.1038/nmat4482. Click here.
  • Islam, M. A., Tchigvintsev, A., Yim, V., Savchenko, A., Yakunin, A. F., Mahadevan, R. and Edwards, E. A. (2016), Experimental validation of in silico model-predicted isocitrate dehydrogenase and phosphomannose isomerase from Dehalococcoides mccartyi. Microbial Biotechnology , 9: 47–60. doi:10.1111/1751-7915.12315. Click here.

2015

  • Ebrahim A., Almaas E., Bauer E., Bordbar A., Burgard A. P., Chang R. L., et al. . (2015). Do genome-scale models need exact solvers or clearer standards? Molecular Systems Biology 11, 831. 10.15252/msb.20156157. Click here.
  • S. Srinivasan, W. R. Cluett and R. Mahadevan, “Constructing kinetic models of metabolism at genome-scales: A review”, Biotechnology Journal. 2015, 10(9):1345-59. Click here.
  • N. Venayak, N. Anesiadis, W. R. Cluett, and R. Mahadevan, “Synthetic Biology Tools for Dynamic Control of Metabolism”, Current Opinion in Biotechnology, 2015, 34C:142-152. Click here.
  • Klamt, R. Mahadevan, On the feasibility of growth-coupled product synthesis in microbial strains, 2015, Metabolic Engineering 30: 166-178. Click here.
  • Nicholas Gold; Christopher M Gowen; Francois-Xavier Lussier; Sarat C Cautha; Radhakrishnan Mahadevan; “Vincent Martin, Metabolic engineering of a tyrosine-overproducing yeast platform using targeted metabolomics”, 2015, Microbial Cell Factories 14(73). Click here.
  • R. Mahadevan, A. von Kamp, S. Klamt; Genome-scale strain designs based on regulatory minimal cut sets, Bioinformatics, Volume 31, Issue 17, 1 September 2015, Pages 2844–2851. Click here.
  • L. Yang, S. Srinivasan, W. R. Cluett, and R. Mahadevan,“ Characterizing metabolic pathway diversification in the context of perturbation size”, Metabolic Engineering, 2015, 28,114-22. Click here.
  • P. Gawand, F. Said-Akbar, N. Venayak, S. Partow, A. E. Motter, R. Mahadevan, “Sub-optimal phenotypes of double-knockout mutants of Escherichia coli depend on the order of gene deletions”, 2015, Integrative Biology, 7(8):930-9. Click here.
  • A. Islam, E. A. Edwards, K. Zengler, R. Mahadevan, and G. Stephanopoulos, “Investigating Moorella thermoacetica Metabolism with a Genome-Scale Constraint-Based Metabolic Model”, 2015, Integrative Biology, 7(8):869-82. Click here.

2014

  • Jayasinghe, N., Franks, A., Nevin, K. P. and Mahadevan, R. (2014), Metabolic modeling of spatial heterogeneity of biofilms in microbial fuel cells reveals substrate limitations in electrical current generation. Biotechnology Journal, 9: 1350–1361. doi:10.1002/biot.201400068. Click here.
  • Islam MA, Waller AS, Hug LA, Provart NJ, Edwards EA, Mahadevan R, New insights into Dehalococcoides mccartyi metabolism from a reconstructed metabolic network-based systems-level analysis of D. mccartyi transcriptomes. PLoS One. 2014 Apr 14;9(4):e94808. doi: 10.1371. Click here.
  • Gawand, P., Mahadevan R., Engineering Escherichia coli for D-ribose production from glucose-xylose mixtures. Industrial Biotechnology, 2014, 10(2): 106-114. Click here.
  • Bourdakos N, Marsili E, Mahadevan R. A defined co-culture of Geobacter sulfurreducens and Escherichia coli in a membrane-less microbial fuel cell. 2014, Biotechnology and Bioengineering. 2014 Apr;111(4):709-18. doi: 10.1002. Click here.

2013

  • Gawand P, Hyland P, Ekins A, Martin VJ, Mahadevan R. Novel approach to engineer strains for simultaneous sugar utilization. 2013, Metabolic Engineering 20, 63-72. Click here.
  • Salimi, F., R. Mahadevan, “Characterizing Metabolic Interactions in a Clostridial Co-culture for Consolidated Bioprocessing”, 2013, BMC Biotechnology, 13(1), 95. Click here.
  • Zhao, J., Scheibe, T. and Mahadevan R. Model-based Analysis of Mixed Uranium(VI) Reduction by Biotic and Abiotic Pathways During in Situ Bioremediation. Chemical Geology, 2013, 357, 215-222. Click here.
  • G. D. Tartakovsky, A. M. Tartakovsky, T. D. Scheibe,Y. Fang, R. Mahadevan, D. R. Lovley, Pore-scale simulation of microbial growth using a genome-scale metabolic model: Implications for Darcy-scale reactive transport. 2013, Advances in Water Resources, 59, 256-270. Click here.
  • P. Hyland, S. M. Lock, R. Mahadevan, “Prediction of Weak Acid Toxicity in Saccharomyces cerevisiae using Genome Scale Metabolic Models”, 2013, Industrial Biotechnology,9 (4), 229-235. Click here.
  • Zheng H, Beliavsky A, Tchigvintsev A, Brunzelle JS, Brown G, Flick R, Evdokimova E, Wawrzak Z, Mahadevan R, Anderson WF, Savchenko A, Yakunin AF, “Structure and activity of the NAD(P)+-dependent succinate semialdehyde dehydrogenase YneI from Salmonella typhimurium.”, 2013, Proteins, 81(6):1031-41. Click here.
  • N. Anesiadis, H.Kobayashi, W. R. Cluett, R. Mahadevan, “Analysis and design of a genetic circuit for dynamic metabolic engineering”, 2013, ACS Synthetic Biology,2(8):442-52. Click here.
  • K. Zhuang, L. Yang, W. Cluett, R. Mahadevan, “Dynamic strain scanning optimization: an efficient strain design strategy for balanced yield, titer, and productivity. DySScO strategy for strain design". 2013, BMC Biotechnology,13:8. Click here.
  • S. Javaherian, N. Anesiadis, R. Mahadevan, A. McGuigan, “Design principles for generating robust gene expression patterns in dynamic engineered tissues”, 2013, Integrative Biology,5(3):578-89. Click here.

2012

  • R. Mahadevan, and M. Henson, “Genome-based Modeling and Design of Metabolic Interactions in Microbial Communities”, 2012, Computational and Structural Biotechnology Journal, 3:4. Click here.
  • Zhuang, K., Ma, E., Lovley, D. R. and Mahadevan, R. (2012), The design of long-term effective uranium bioremediation strategy using a community metabolic model. Biotechnology & Bioengineering., 109: 2475–2483. doi:10.1002/bit.24528 Click here.
  • Suzuki, H., MacDonald, J., Khajamhoidddin, S., Salamov A., Hori C., Aerts, A., Henrissat, B., Wiebenga, A., Barry, K., Lindquist, E., Labutti, K., Lapidus, A., Lucas, S., Coutinho, P., Gong, Y., Samejima, M., Mahadevan R., Abou-Zaid, M., de Vries, R., Igarashi, K., Yadav, J., Grigoriev, I., and E. R. Master, “ Comparative genomics of the white rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize. 2012, 13:444, BMC Genomics. Click here.
  • Facchini, P., J. Bohlmann, P.S. Covello, V. De Luca, R. Mahadevan, J.E. Page, D.-K. Ro, C.W. Sensen. R. Storms, and V.J.J. Martin. Synthetic biosystems for the production of high-value plant metabolites. 2012, 30(3), 127-131. Trends in Biotechnology. Click here.
  • Barlett, M., Zhuang, K., Mahadevan, R., and Lovley, D.: Integrative analysis of Geobacter spp. and sulfate-reducing bacteria during uranium bioremediation, Biogeosciences, 9, 1033-1040, https://doi.org/10.5194/bg-9-1033-2012, 2012. Click here.
  • Khazaei T, McGuigan A, Mahadevan R. "Ensemble Modeling of Cancer Metabolism". Frontiers in Physiology. 2012;3:135. doi:10.3389/fphys.2012.00135. Click here.

2011

  • D. Pinel. P. Gawand, R. Mahadevan, V. Martin, “‘Omics’ technologies and systems biology for engineering Saccharomyces cerevisiae strains for lignocellulosic bioethanol production". 2012, 30(3), 127-131. Biofuels. Click here.
  • A. V. Pandit and R. Mahadevan, “An in silico Characterization of  Microbial Electrosynthesis for Metabolic Engineering of Biochemicals”. Microbial Cell Factories, 2011, 10:76. Click here.
  • J. Usher, V. Balderas, A. Johnston, P. Quon, N. Gold, V. Martin, L. Harris, R. Mahadevan and K. Baetz, “Chemical and synthetic genetic array analysis identifies genes that suppress xylose utilization and fermentation in Saccharomyces cerevisiae. 2011,1, 247:258, G3 : Genes, Genomes, Genetics. Click here.
  • L. Yang, W. R. Cluett, and R. Mahadevan, “EMILiO: A fast algorithm for genome-scale strain design”. 2011, 13(3):272-281. Metabolic Engineering. Click here.
  • K. Zhuang, G. Vemuri, R. Mahadevan, "Economics of Membrane Occupancy and the Respiro-fermentation,” Molecular Systems Biology, 2011, 7:500. Click here.
  • J. Zhao, and R. Mahadevan, “Model-based analysis of the role of biological, hydrological and geochemical factors affecting uranium bioremediation affecting uranium bioremediation”, Biotechnology and Bioengineering, 2011, 108(7):1537-1548. Click here.
  • Y. Fang, T. D. Scheibe, R. Mahadevan, S. Garg, P. E. Long, and D. R. Lovley, “Direct Coupling of a Genome-Scale Microbial in silico model and a groundwater reactive transport model”, Journal of Contaminant Hydrology, 2011, 122(1-4):96-103. Click here.
  • R. Mahadevan, B. Palsson, and D. Lovley, “In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale  modeling”, Nature Reviews Microbiology, 2011, 9(1), 39-50. Click here.

2010 and Before

  • A. Islam, E. Edwards, and R. Mahadevan, “Characterizing the Metabolism of Dehalococcoides with a Constraint-Based Model”, PLoS Computational Biology, 2010,6(8). Click here.
  • F. Salimi, K. Zhuang and R. Mahadevan, “Genome-scale Metabolic Modeling of a Clostridial Co-culture for Consolidated Bioprocessing”, Biotechnology Journal, 2010,5(7):726-738. Click here.
  • S. Garg, L. Yang, and R. Mahadevan, “Thermodynamic analysis of regulation in metabolic networks using constraint-based modeling”, BMC Research Notes, 2010, 3:125. Click here.
  • K. Srinivasan, R. Mahadevan, “Characterization of Proton Production and Consumption Associated with Microbial Metabolism”, BMC Biotechnology , 2010, 10:2. Click here.
  • J. Zhao, T.D. Scheibe, Y. Fang, D.R. Lovley, R. Mahadevan, “ Modeling and sensitivity analysis of electron capacitance for Geobacter in sedimentary environments”, Journal of Contaminant Hydrology, 2010, 112(1-4):30-44. Click here.
  • C. Risso, J. Sun, K. Zhuang, R. Mahadevan, D. R. Lovley et al., “ Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer Rhodoferax ferrireducens . ”, BMC Genomics, 2009, 10:447. Click here.
  • T.D. Scheibe, R. Mahadevan, Y. Fang, S. Garg, P. Long, and D.R. Lovley, “ Coupling a Genome-scale Metabolic Model with a Reactive Transport Model to describe in situ uranium bioremediation. ”, Microbial Biotechnology, 2009, 2(2):274-86. Click here.
  • J. Sun, B. Sayyar, J.E. Butler, P. Pharkya, T.R.Fahland,I. Famili, C.H. Schilling, D.R. Lovley, and R. Mahadevan, “ Genome-scale constraint-based modeling of Geobacter metallireducens ”, BMC Systems Biology, 2009, 3:15. Click here.
  • N. Anesiadis, W. R. Cluett, and R. Mahadevan, “ Dynamic Metabolic Engineering for Increasing Bioprocess Productivity”, Metabolic Engineering, 2008,10(5):255-66. Click here.
  • M. Izallalen, R. Mahadevan, A. Burgard, B. Postier, R. didonato Jr., J. Sun, C. H. Schilling, and D. R. Lovley, “ Geobacter sulfurreducens Strain Engineered for Increased Rates of Respiration”, Metabolic Engineering, 2008, 10(5):267-75. Click here.
  • L. Yang, W. R. Cluett and R. Mahadevan, “A Bilevel Optimization Algorithm to Identify Enzymatic Capacity Constraints in Metabolic Networks”, Computers and Chemical Engineering,2008, 32(9):2072-2085. Click here.
  • P. Dhurjati and R. Mahadevan, “ Systems Biology: A Synergistic Interplay Between Biology and Mathematics”, Canadian Journal of Chemical Engineering, 2008,86(2):127-141. Click here.
  • R. Mahadevan, B. Yan, B. Postier, K. P. Nevin, T. L. Woodard, R. O Neil, M. Coppi, B. Methe, J. Krushkal, “ Characterizing Regulation of Metabolism in Geobacter sulfurreducens through Genome-wide Expression Data and Sequence Analysis”, Omics, 2008,12(1):33-59. Click here.
  • R. Mahadevan and D. R. Lovley, “The Degree of Redundancy in Metabolic Genes Is Linked to Mode of Metabolism”, Biophysical Journal, 2008, 94(4):1216-20. Click here.
  • D. Segura, D. R. Lovley, and R. Mahadevan, “Computational and Experimental Analysis of Redundancy in the Central Metabolism of Geobacter sulfurreducens”, PLoS Computational Biology, 2008, 4(1):e36. Click here.
  • Y.K. Oh, S. M. Park, B.O. Palsson, C. H. Schilling and R. Mahadevan, “Genome-scale Reconstruction of Metabolic Network in Bacillus subtilis Based on High-throughput Phenotyping and Gene Essentiality Data”, Journal of Biological Chemistry, 2007, 282(39):28791-9. Click here.
  • J. L. Hjersted, R. Mahadevan, and M. A. Henson,“Genome-scale analysis of Saccharomyces cerevisiae metabolism and ethanol production in fed-batch culture”, Biotechnology and Bioengineering, 2007, 97 (5), 1190-204. Click here.
  • K. G. Gadkar, R. Mahadevan, and F. J. Doyle III, “Batch Control of Genetic Alterations for Optimal Metabolic Engineering”, Automatica, 2006, Oct; 42(10), 1723-1733. Click here.
  • R. Mahadevan, C. H. Schilling, D. R. Bond, D. R. Lovley, “Characterization of metabolism in the Fe (III)-reducing organism Geobacter sulfurreducens by constraint-based modeling”, Applied and Environmental Microbiology, 2006, 72(2), 1558-1568. Click here.
  • R. Mahadevan, A. P. Burgard, I. Famili, S. Van Dien, and C. H. Schilling, “Applications of Metabolic Modeling to drive Bioprocess Development for the production of Value-Added Chemicals”, Biotechnology and Bioprocess Engineering, 2005, 10:408-417. Click here.
  • I. Famili, R. Mahadevan, and B. O. Palsson, “k-Cone Analysis: Determining All Candidate Values for Kinetic Parameters on a Network-scale”, Biophysical Journal, 2005, 88(3), 1616-25. Click here.
  • R. Mahadevan, and B. O. Palsson, “Properties of Large-Scale Biochemical Networks: Structure vs. Function”, Biophysical Journal, 2005, 88(1), L07-L09. Click here.
  • K. G. Gadkar, F. J Doyle III, J. S. Edwards, and R. Mahadevan, “Estimating optimal profiles of genetic alterations using constraint‐based models”, Biotechnology and Bioengineering, 2005, 89(2), 243-251. Click here.
  • S. J. Wiback, R. Mahadevan, and B. O. Palsson, “Using Metabolic Flux Data to Further Constrain the Metabolic Solution Space and Predict Internal Flux Patterns: The Escherichia coli -Spectrum”, Biotechnology and Bioengineering, 2004, 86(3), 317-331. Click here.
  • R. Mahadevan, C. H. Schilling, “ Effects of Alternate Optimal Solutions in Constraint-based Genome Scale Metabolic Models”, Metabolic Engineering, 2003, 5:264-276. Click here.
  • S. J. Wiback, R. Mahadevan, and B. O. Palsson, “Reconstructing metabolic flux vectors from extreme pathways: defining the α-spectrum”, Journal of Theoretical Biology, 2003, 224:313-324. Click here.
  • R. Mahadevan and F. J. Doyle III, “On-line Optimization of a Recombinant Product in a Fed-batch Bioreactor ”, Biotechnology Progress, 2003, 19(2), 639-646. Click here.
  • R. Mahadevan and F. J. Doyle III, “Efficient Optimization Approaches to Nonlinear Model Predictive Control”, International Journal of Robust and Nonlinear Control, 2003, 13 (3-4): 309-329. Click here.
  • R. Mahadevan, J. S. Edwards, and F. J. Doyle III, “Dynamic Flux Balance Analysis Approaches”, Biophysical Journal, 2002, 83, 1331-1340. Click here.
  • R. Mahadevan, A. C. Allcock, and F. J. Doyle III, “Control-relevant Scheduling of Polymer Grade Transitions”, AIChE Journal, 2002, 48(8), 1754-1764. Click here.
  • Mahadevan R., Agrawal S. K., and Doyle III F. J., “Differential Flatness based Nonlinear Predictive Control of Fed-batch Bioreactors”, Control Engineering Practice, 2001, 9(8), 889-899. Click here.